From 5c18b75cc548bd446ef40f765d13cb92b539ae7c Mon Sep 17 00:00:00 2001 From: aliciaaevans Date: Fri, 7 Jun 2024 16:17:30 -0400 Subject: [PATCH 01/24] rebuild bowtie --- recipes/bowtie/build_failure.osx-64.yaml | 104 ----------------------- recipes/bowtie/meta.yaml | 1 - 2 files changed, 105 deletions(-) delete mode 100644 recipes/bowtie/build_failure.osx-64.yaml diff --git a/recipes/bowtie/build_failure.osx-64.yaml b/recipes/bowtie/build_failure.osx-64.yaml deleted file mode 100644 index 52d72157ec1d0..0000000000000 --- a/recipes/bowtie/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c2a8312eada5f447d81c5780f388e40fc17487b8966607e43b2708bd9986e45b # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: false # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - In file included from /opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/_build_env/bin/../include/c/v1/__std_mbstate_t.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/_build_env/bin/../include/c/v1/__mbstate_t.h:45: - /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/sys/_types/_mbstate_t.h:31:9: error: unknown type name '__darwin_mbstate_t' - typedef __darwin_mbstate_t mbstate_t; - ^ - In file included from bowtie_build_main.cpp:13: - ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] - int thru = 0; - ^ - 1 warning and 1 error generated. - make: *** [Makefile:237: bowtie-build-s] Error 1 - Extracting download - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bowtie/rename_version_to_version_txt.patch - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bowtie/rename_version_to_version_txt.patch with args: - ['-Np1', '-i', '/tmp/tmp1sqf2v3x/rename_version_to_version_txt.patch.native', '--binary'] - Patch analysis gives: - [[ RA-MD1LOVE ]] - [[ rename_version_to_version_txt.patch ]] - - Key: - - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - R :: Reversible A :: Applicable - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/work/conda_build.sh']' returned non-zero exit status 2. - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - x86_64-apple-darwin13.4.0-clang -O3 -DCOMPILER_OPTIONS="\"-O3 -DPOPCNT_CAPABILITY -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix \"" -DPOPCNT_CAPABILITY -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix \ - -fno-strict-aliasing -DBOWTIE_VERSION="\"cat VERSION.txt\"" -DBUILD_HOST="\"hostname\"" -DBUILD_TIME="\"2024-06-07T16:59:50\"" -DCOMPILER_VERSION="\"x86_64-apple-darwin13.4.0-clang -v 2>&1 | tail -1\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ - -I third_party \ - -o bowtie-build-s ebwt_build.cpp \ - ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp bowtie_build_main.cpp \ - -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lpthread -# Last 100 lines of the build log. diff --git a/recipes/bowtie/meta.yaml b/recipes/bowtie/meta.yaml index 069e9a1bd54ef..32cfcadbc62c2 100644 --- a/recipes/bowtie/meta.yaml +++ b/recipes/bowtie/meta.yaml @@ -12,7 +12,6 @@ source: - rename_version_to_version_txt.patch build: - skip: True # [py<30] number: 8 run_exports: - {{ pin_subpackage("bowtie", max_pin="x.x") }} From 74941e03b852958792da304e8702270852f235a5 Mon Sep 17 00:00:00 2001 From: aliciaaevans Date: Fri, 7 Jun 2024 16:32:02 -0400 Subject: [PATCH 02/24] exclude branches that start with bulk --- .circleci/config.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 6bcdb1d063e65..1046e0d9acbe5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -229,6 +229,7 @@ workflows: ignore: - master - bulk + - /bulk.*/ matrix: parameters: os: From 5b27f645c3496835d2ad43abc1232232eb9c84e9 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 20:47:22 -0400 Subject: [PATCH 03/24] macOS SDK attempt --- .github/workflows/Bulk.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 539fb05adf79b..85070f17a0892 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -63,6 +63,12 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda + + # see if we can convince SDK 10.13 + MACOSX_SDK_VERSION=10.13 + plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist + plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist + echo '============' conda info --all conda config --show-sources From eeed429a1061bafd8b1c68de7ae198940ce30706 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 20:51:44 -0400 Subject: [PATCH 04/24] test --- .github/workflows/Bulk.yml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 85070f17a0892..b73045464f82e 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -64,11 +64,6 @@ jobs: eval "$(conda shell.bash hook)" conda activate bioconda - # see if we can convince SDK 10.13 - MACOSX_SDK_VERSION=10.13 - plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist - plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist - echo '============' conda info --all conda config --show-sources @@ -143,6 +138,12 @@ jobs: # The SDK isn't actually cached, so reinstall it run_conda_forge_build_setup + # see if we can convince SDK 10.13 + MACOSX_SDK_VERSION=10.13 + plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist + plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist + + echo '============' conda info --all conda config --show-sources From 5b8d7dcfaf1b0064e26d3f5920e5dd0b42422b2f Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 20:52:57 -0400 Subject: [PATCH 05/24] test --- .github/workflows/Bulk.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index b73045464f82e..8d83aa786e89a 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -2,7 +2,7 @@ name: Bulk branch on: push: branches: - - bulk + - bulk-osx-failures jobs: build-linux: name: Bulk Linux Builds From 346753ff2ec9afe8853669920dae3ca305b618c2 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 21:01:29 -0400 Subject: [PATCH 06/24] [ci run] --- .github/workflows/Bulk.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 8d83aa786e89a..9be1a0e085472 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -63,7 +63,6 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda - echo '============' conda info --all conda config --show-sources From 6d0884b6ac5cbf2bc6df82df1f5185c94dcdec3e Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 21:06:12 -0400 Subject: [PATCH 07/24] test --- .github/workflows/Bulk.yml | 77 ++------------------------------------ 1 file changed, 4 insertions(+), 73 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 9be1a0e085472..2a387f3ab774c 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -4,75 +4,6 @@ on: branches: - bulk-osx-failures jobs: - build-linux: - name: Bulk Linux Builds - if: "contains(github.event.head_commit.message, '[ci run]')" - runs-on: ubuntu-latest - strategy: - fail-fast: false - max-parallel: 6 - matrix: - runner: [0, 1, 2, 3, 4, 5] - steps: - - uses: actions/checkout@v4 - with: - # checkout as BiocondaBot in order to have the permission to push fail logs - token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} - - - name: set git user - run: | - git config user.name BiocondaBot - git config user.email BiocondaBot@users.noreply.github.com - - - name: set path - run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH - - - name: Fetch conda install script - run: | - wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh - - - name: Restore cache - id: cache - uses: actions/cache@v4 - with: - path: /opt/mambaforge - key: ${{ runner.os }}--bulk--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }} - - - name: Set up bioconda-utils - if: steps.cache.outputs.cache-hit != 'true' - run: bash install-and-set-up-conda.sh - - # This script can be used to reconfigure conda to use the right channel setup. - # This has to be done after the cache is restored, because - # the channel setup is not cached as it resides in the home directory. - # We could use a system-wide (and therefore cached) channel setup, - # but mamba does not support that at the time of implementation - # (it ignores settings made with --system). - - name: Configure conda - run: bash configure-conda.sh - - - name: Build and upload - env: - ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} - INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} - QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} - # Mimic circleci - OSTYPE: "linux-gnu" - CI: "true" - run: | - set -e - eval "$(conda shell.bash hook)" - conda activate bioconda - echo '============' - conda info --all - conda config --show-sources - python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' - echo '============' - bioconda-utils build recipes config.yml \ - --worker-offset ${{ matrix.runner }} --n-workers 6 \ - --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ - --lint --record-build-failures --skiplist-leafs - conda clean -y --all build-osx: name: Bulk OSX Builds @@ -80,9 +11,9 @@ jobs: runs-on: macos-13 strategy: fail-fast: false - max-parallel: 4 + max-parallel: 1 matrix: - runner: [0, 1, 2, 3] + runner: [0] #, 1, 2, 3] steps: - uses: actions/checkout@v4 with: @@ -150,6 +81,6 @@ jobs: python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' echo '============' bioconda-utils build recipes config.yml \ - --worker-offset ${{ matrix.runner }} --n-workers 4 \ - --lint --anaconda-upload --record-build-failures --skiplist-leafs + --worker-offset ${{ matrix.runner }} --n-workers 1 \ + --lint conda clean -y --all From 6f9d75f60c4937f3508859c1f2e5136b6ae155a5 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 21:06:51 -0400 Subject: [PATCH 08/24] [ci run] --- .github/workflows/Bulk.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 2a387f3ab774c..97a331799869f 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -73,7 +73,6 @@ jobs: plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist - echo '============' conda info --all conda config --show-sources From d86a126ab506bfd622060b05a8fcef75ec28e244 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 21:14:58 -0400 Subject: [PATCH 09/24] [ci run] --- .github/workflows/Bulk.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 97a331799869f..e43a413a58140 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -79,7 +79,5 @@ jobs: conda activate bioconda python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' echo '============' - bioconda-utils build recipes config.yml \ - --worker-offset ${{ matrix.runner }} --n-workers 1 \ - --lint + bioconda-utils build recipes config.yml --packages bowtie conda clean -y --all From d16adf05d7c3f13eb31810b5da8198fc0ce59655 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 21:26:41 -0400 Subject: [PATCH 10/24] [ci run] --- .github/workflows/Bulk.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index e43a413a58140..a65fe08efbf3d 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -65,13 +65,12 @@ jobs: eval "$(conda shell.bash hook)" conda activate bioconda - # The SDK isn't actually cached, so reinstall it - run_conda_forge_build_setup - # see if we can convince SDK 10.13 MACOSX_SDK_VERSION=10.13 - plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist - plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist + MACOSX_DEPLOYMENT_TARGET=10.13 + + # The SDK isn't actually cached, so reinstall it + run_conda_forge_build_setup echo '============' conda info --all From b2fdf0df9c16a448ae41a866f0f16a9eeb58b834 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 21:51:50 -0400 Subject: [PATCH 11/24] [ci run] --- .github/workflows/Bulk.yml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index a65fe08efbf3d..d9e5e8e2fc289 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -65,12 +65,16 @@ jobs: eval "$(conda shell.bash hook)" conda activate bioconda - # see if we can convince SDK 10.13 - MACOSX_SDK_VERSION=10.13 - MACOSX_DEPLOYMENT_TARGET=10.13 + # https://github.com/conda-forge/conda-forge-ci-setup-feedstock/ + export MACOSX_SDK_VERSION=10.13 + export MACOSX_DEPLOYMENT_TARGET=10.13 + url="https://github.com/alexey-lysiuk/macos-sdk/releases/download/${MACOSX_SDK_VERSION}/MacOSX${MACOSX_SDK_VERSION}.tar.xz" + curl -L --output MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz "${url}" + export CONDA_BUILD_SYSROOT="${OSX_SDK_DIR}/MacOSX${MACOSX_SDK_VERSION}.sdk" + tar -xf MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz -C "$(dirname "$CONDA_BUILD_SYSROOT")" - # The SDK isn't actually cached, so reinstall it - run_conda_forge_build_setup + plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist + plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist echo '============' conda info --all From d8f7ab2ee9b091d2f396addbe7c035546eb9537e Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Fri, 7 Jun 2024 21:57:47 -0400 Subject: [PATCH 12/24] [ci run] --- .github/workflows/Bulk.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index d9e5e8e2fc289..f91983956d191 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -65,6 +65,7 @@ jobs: eval "$(conda shell.bash hook)" conda activate bioconda + set -x # https://github.com/conda-forge/conda-forge-ci-setup-feedstock/ export MACOSX_SDK_VERSION=10.13 export MACOSX_DEPLOYMENT_TARGET=10.13 @@ -75,6 +76,7 @@ jobs: plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist + set +x echo '============' conda info --all From fcf7e580fd15a50642da7484de05448fc3ce21d9 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 13:04:10 +0000 Subject: [PATCH 13/24] [ci run] --- .github/workflows/Bulk.yml | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index f91983956d191..dfe03aff4a24b 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -59,24 +59,12 @@ jobs: QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} # Mimic circleci OSTYPE: "darwin" - CI: "true" + # CI: "true" run: | set -e eval "$(conda shell.bash hook)" conda activate bioconda - - set -x - # https://github.com/conda-forge/conda-forge-ci-setup-feedstock/ - export MACOSX_SDK_VERSION=10.13 - export MACOSX_DEPLOYMENT_TARGET=10.13 - url="https://github.com/alexey-lysiuk/macos-sdk/releases/download/${MACOSX_SDK_VERSION}/MacOSX${MACOSX_SDK_VERSION}.tar.xz" - curl -L --output MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz "${url}" - export CONDA_BUILD_SYSROOT="${OSX_SDK_DIR}/MacOSX${MACOSX_SDK_VERSION}.sdk" - tar -xf MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz -C "$(dirname "$CONDA_BUILD_SYSROOT")" - - plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist - plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist - set +x + run_conda_forge_build_setup_osx echo '============' conda info --all From b2ab90cf7c8746e642ecac3b9eeb87bfe4c0d6c1 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 13:23:00 +0000 Subject: [PATCH 14/24] [ci run] --- .github/workflows/Bulk.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index dfe03aff4a24b..ea5f11269afa4 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -64,7 +64,9 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda - run_conda_forge_build_setup_osx + export MACOSX_SDK_VERSION=10.13 + export MACOSX_DEPLOYMENT_TARGET=10.13 + run_conda_forge_build_setup echo '============' conda info --all From d46b1106e7910cf116a8088084d2f40b1186c533 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 13:47:58 +0000 Subject: [PATCH 15/24] [ci run] --- .github/workflows/Bulk.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index ea5f11269afa4..86d949cd082fa 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -64,8 +64,8 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda - export MACOSX_SDK_VERSION=10.13 - export MACOSX_DEPLOYMENT_TARGET=10.13 + # export MACOSX_SDK_VERSION=10.13 + # export MACOSX_DEPLOYMENT_TARGET=10.13 run_conda_forge_build_setup echo '============' From b61d168d038d3bda1a588fbe292e436c84bcb47d Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 13:59:50 +0000 Subject: [PATCH 16/24] [ci run] --- .github/workflows/Bulk.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 86d949cd082fa..3cc4bd074bcce 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -59,13 +59,13 @@ jobs: QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} # Mimic circleci OSTYPE: "darwin" - # CI: "true" + CI: "true" run: | set -e eval "$(conda shell.bash hook)" conda activate bioconda - # export MACOSX_SDK_VERSION=10.13 - # export MACOSX_DEPLOYMENT_TARGET=10.13 + export MACOSX_SDK_VERSION=10.13 + export MACOSX_DEPLOYMENT_TARGET=10.13 run_conda_forge_build_setup echo '============' From 85fe91108be4c786d990b28fb08db54f71dbe7d1 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 14:45:43 +0000 Subject: [PATCH 17/24] [ci run] --- .github/workflows/Bulk.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 3cc4bd074bcce..f51cb82683934 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -64,7 +64,7 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda - export MACOSX_SDK_VERSION=10.13 + # export MACOSX_SDK_VERSION=10.13 export MACOSX_DEPLOYMENT_TARGET=10.13 run_conda_forge_build_setup From ffbfc9772c67b7d39e68995a3173baa1020747bf Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 15:03:10 +0000 Subject: [PATCH 18/24] [ci run] --- .github/workflows/Bulk.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index f51cb82683934..cc7a1fc368141 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -64,8 +64,7 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda - # export MACOSX_SDK_VERSION=10.13 - export MACOSX_DEPLOYMENT_TARGET=10.13 + MACOSX_DEPLOYMENT_TARGET=10.13 run_conda_forge_build_setup echo '============' From dbdb03daa5756a16c27ae21141643008b3fa03dc Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 15:24:48 +0000 Subject: [PATCH 19/24] [ci run] --- .github/workflows/Bulk.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index cc7a1fc368141..5277f6a916971 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -64,7 +64,10 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda - MACOSX_DEPLOYMENT_TARGET=10.13 + set -x + echo $MACOSX_SDK_VERSION + echo $MACOSX_DEPLOYMENT_TARGET + exit 1 run_conda_forge_build_setup echo '============' From 478c68bcaa37b7be55fc17a67bffcfefe07c46c7 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 15:31:42 +0000 Subject: [PATCH 20/24] [ci run] --- .github/workflows/Bulk.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 5277f6a916971..81cd891911667 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -65,10 +65,10 @@ jobs: eval "$(conda shell.bash hook)" conda activate bioconda set -x + run_conda_forge_build_setup echo $MACOSX_SDK_VERSION echo $MACOSX_DEPLOYMENT_TARGET exit 1 - run_conda_forge_build_setup echo '============' conda info --all From f704610731e855de99a908dd16627b81639e4aac Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 15:41:05 +0000 Subject: [PATCH 21/24] [ci run] --- .github/workflows/Bulk.yml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 81cd891911667..8c008c780372e 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -30,7 +30,7 @@ jobs: - name: Fetch conda install script run: | - wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh + wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk-osx-failures/{common,install-and-set-up-conda,configure-conda}.sh - name: Restore cache id: cache @@ -64,11 +64,8 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda - set -x + source common.sh run_conda_forge_build_setup - echo $MACOSX_SDK_VERSION - echo $MACOSX_DEPLOYMENT_TARGET - exit 1 echo '============' conda info --all From f3c8244d3182f56889cc1b0c7ec4662879af2b3a Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 16:14:41 +0000 Subject: [PATCH 22/24] [ci run] --- .github/workflows/Bulk.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 8c008c780372e..21b3a44c1b384 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -64,9 +64,12 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda + set -x source common.sh run_conda_forge_build_setup - + echo $MACOSX_DEPLOYMENT_TARGET + echo $MACOSX_SDK_VERSION + exit 1 echo '============' conda info --all conda config --show-sources From 9ec27764dc72d5950c6192ca8e7a1f205b1cb37c Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 16:25:25 +0000 Subject: [PATCH 23/24] [ci run] --- .github/workflows/Bulk.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 21b3a44c1b384..6d5215232c0f1 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -64,12 +64,8 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda - set -x source common.sh run_conda_forge_build_setup - echo $MACOSX_DEPLOYMENT_TARGET - echo $MACOSX_SDK_VERSION - exit 1 echo '============' conda info --all conda config --show-sources From 7fbfefe93cf755cb95101b34211756654095fb3b Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 16:35:40 +0000 Subject: [PATCH 24/24] [ci run] --- .github/workflows/Bulk.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 6d5215232c0f1..759c9db624c58 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -66,6 +66,8 @@ jobs: conda activate bioconda source common.sh run_conda_forge_build_setup + echo $MACOSX_DEPLOYMENT_TARGET + echo $MACOSX_SDK_VERSION echo '============' conda info --all conda config --show-sources